Editor's Note: The Iraq Special Operations Forces (ISOF) is probably the largest special forces outfit ever built by the United States, and it is free of many of the controls that most governments employ to rein in such lethal forces. Research support provided by the Investigative Fund of The Nation Institute, the Center for Investigative Reporting, and New American Media. NAM Middle East correspondent Shane Bauer spent early 2009 reporting from Iraq. This article was first published in The Nation.

New America Media – The light is fading from the dusty Baghdad sky as Hassan Mahsan re-enacts what happened to his family last summer. We're standing in the courtyard of his concrete-block house, his children are watching us quietly, and his wife is twirling large circles of dough and slapping them against the inside walls of a roaring oven. He walks over to his three-foot-tall daughter and grabs her head like a melon. As she stands there, he gestures wildly behind her, pretending to tie up her hands, then pretending to point a rifle at her head. "They took the blindfold off me, pointed the gun at her head and cocked it, saying, 'Either you tell us where al-Zaydawi is, or we kill your daughter.'"

"They just marched into our house and took whatever they wanted," Hassan's mother says, peeking out the kitchen door. "I've never seen anyone act like this."

As Hassan tells it, it was a quiet night on June 10, 2008, in Sadr City, Baghdad's poor Shia district of more than 2 million people, when the helicopter appeared over his house and the front door exploded, nearly burning his sleeping youngest son. Before Hassan knew it, he was on the ground, hands bound and a bag over his head, with eight men pointing rifles at him, locked and loaded.

At first he couldn't tell whether the men were Iraqis or Americans. He says he identified himself as a police sergeant, offering his ID before they took his pistol and knocked him to the ground. The men didn't move like any Iraqi forces he'd ever seen. They looked and spoke like his countrymen, but they were wearing American-style uniforms and carrying American weapons with night-vision scopes. They accused him of being a commander in the local militia, the Mahdi Army, before they dragged him off, telling his wife he was "finished." But before they left, they identified themselves. "We are the Special Forces. The dirty brigade," Hassan recalls them saying.

The Iraq Special Operations Forces (ISOF) is probably the largest special forces outfit ever built by the United States, and it is free of many of the controls that most governments employ to rein in such lethal forces. The project started in the deserts of Jordan just after the Americans took Baghdad in April 2003. There, the US Army's Special Forces, or Green Berets, trained mostly 18-year-old Iraqis with no prior military experience. The resulting brigade was a Green Beret's dream come true: a deadly, elite, covert unit, fully fitted with American equipment, that would operate for years under US command and be unaccountable to Iraqi ministries and the normal political process.

According to Congressional records, the ISOF has grown into nine battalions, which extend to four regional "commando bases" across Iraq. By December, each will be complete with its own "intelligence infusion cell", which will operate independently of Iraq's other intelligence networks. The ISOF is at least 4,564 operatives strong, making it approximately the size of the US Army's own Special Forces in Iraq. Congressional records indicate that there are plans to double the ISOF over the next "several years."

According to retired Lt. Col. Roger Carstens, US Special Forces are "building the most powerful force in the region." In 2008 Carstens, then a senior fellow at the Center for a New American Security, was an adviser to the Iraqi National Counter-Terror Force, where he helped set up the Iraqi counterterrorism laws that govern the ISOF.

"All these guys want to do is go out and kill bad guys all day," he says, laughing. "These guys are sh*t hot. They are just as good as we are. We trained 'em. They are just like us. They use the same weapons. They walk like Americans."

When the US Special Forces began the slow transfer of the ISOF to Iraqi control in April 2007, they didn't put it under the command of the Defense Ministry or the Interior Ministry, bodies that normally control similar special forces the world over. Instead, the Americans pressured the Iraqi government to create a new minister-level office called the Counter-Terrorism Bureau.

Established by a directive from Iraqi Prime Minister Nuri al-Maliki, the CTB answers directly to him and commands the ISOF independently of the police and army. According to Maliki's directive, the Iraqi Parliament has no influence over the ISOF and knows little about its mission. US Special Forces operatives like Carstens have largely overseen the bureau. Carstens says this independent chain of command "might be the perfect structure" for counterterrorism worldwide.

Although the force is officially controlled by the Iraqi government, popular perception in Baghdad is that the ISOF – the dirty brigade – is a covert, all-Iraqi branch of the US military. That reading isn't far from the truth. The US Special Forces are still closely involved with every level of the ISOF, from planning and carrying out missions to deciding tactics and creating policy. According to Brig. Gen. Simeon Trombitas, commander of the Iraq National Counter-Terror Force Transition Team, part of the multinational command responsible for turning control of the ISOF over to the Iraqi government, the US Special Forces continue to "have advisers at every level of the chain of command."

In January 2008, the US Special Forces started allowing ISOF commanders to join missions with them and the ISOF rank and file. Starting last summer – when Hassan's family was attacked – ISOF battalions began launching missions on their own, without American advisers, in Sadr City, where political agreements forbid the Americans from entering. Accusations of human rights abuses, killings, and politically motivated arrests have surfaced, including assaults on a university president and arrests of opposition politicians.

The US government has been focused on turning out "as many men in arms as possible, as quickly as possible," says Peter Harling, senior Middle East analyst at the International Crisis Group. "There has been very little impetus to build checks and controls to prevent abuse. It's been very much about building up capability without the oversight that could prevent some of the units [from] turning into proxies working for some politician."

In Sadr City, opposition to the Iraqi government and the US occupation is strong. There is no longer any visible militia presence, but pictures of anti-American cleric Muqtada al-Sadr still stick to the US-built concrete walls that enclose the city, and calls to prayer end with a demand for the hastened exit of "the enemy". There, the ISOF uses a policy of collective punishment, aimed at intimidating civilians, charges Hassan al-Rubaie, Sadrist member of the parliamentary Security and Defense Committee. "They terrorize entire neighborhoods just to arrest one person they think is a terrorist," he says. "This needs to stop."

US Special Forces advisers have done little to respond to allegations of abuse. Civilian pleas, public protests, complaints by Iraqi Army commanders about the ISOF's actions, and calls for disbanding it by members of Parliament have not pushed the US government to take a hard look at the force they are creating. Instead, US advisers dismiss such claims as politically motivated. "The enemy is trying to discredit them," says Carstens. "It's not because they are doing anything dirty."

On the same night Hassan Mahsan's house was raided, 26-year-old Haidar al-Aibi was killed with a bullet to the forehead. His family says there was no warning. They tell me how it happened as we drink tea on the floor of their living room, furnished only with thick foam cushions and mournful depictions of the Shiite martyr Hussain [peace be upon him]. A woman weeps loudly in the corner, the sleeping child of her dead son almost obscured by the folds of her black garments.

Fathil al-Aibi says the family was awakened around midnight by a nearby explosion. His brother Haidar ran up to the roof to see what had happened and was immediately shot from a nearby rooftop. When Fathil, his brother Hussein, and his father Abbas tried to bring Haidar downstairs, they were shot at too. For about two hours, he lay lifeless on the roof, while his family panicked as red laser beams from rifle scopes danced on their windows. "We had tests the next day at the university," Hussein says. "We didn't think he would go like this."

Down the road, around the same time that night, police commando Ahmed Shibli says he was also being fired on. He illuminates two bullet holes in his house with a kerosene lamp as we talk. The men who busted open his front door called themselves the dirty brigade, he says, and they were carrying American weapons, not the AK-47s or PKCs the National Police use. When they entered, they fired immediately. "It wasn't a warning shot. They shot at me like they wanted to kill me as I was getting down on the ground. It was like we were first-degree terrorists." They fired again, he says, fatally shooting his ailing 63-year-old father. As blood poured from the old man's hip, Ahmed says the men held a gun to his little boy's head and forced his wife to search the room for the police-issued weapon he had left at work.

Ahmed and his brother were hauled to the outskirts of the city, along with Hassan, where they were lined up with other men in the dark. Hassan insists on substantiating his story by showing me an official complaint issued by a local army commander named Mustafa Sabah Yunis, alleging that an "unknown armed squadron" entered the area and arrested him.

Meanwhile, the Iraqi Army was rushing in to respond to the gunfire, and according to Hussein al-Aibi, these soldiers were shot at as well. He tells me the army got Haidar off the roof and drove him to the hospital. On the way, Fathil says, the vehicle was stopped by a dirty brigade operative, who asked Iraqi Army Major Abu Rajdi where they were going. According to Fathil, Rajdi told the operative, "This is a college student who has nothing to do with anything, and you shot him recklessly." The operative responded by hitting Rajdi and saying, "Turn around and go back, or we'll shoot him and we'll shoot you too."

At Haidar's funeral, Fathil asked Rajdi to testify. "You are a representative of the government, and you saw it all happen," he told the major. "You saw that he didn't have a weapon in his hand." Fathil says the major declined. "This is the dirty brigade," he recalls Rajdi saying. "We are afraid of them. When we see them, we retreat. If I testify against them, I'll be killed the next day. They kill and no one will hold them accountable, because they belong to the Americans."

Major Rajdi's fear and distrust of the ISOF are echoed by other members of the regular Iraqi Army. "Sometimes we are surprised when the Special Forces enter," says Lt. Colonel Yahya Rasoul Abdullah, commander of the Third Battalion of the Forty-second Brigade in Sadr City. "Bad things happen. Some people steal, and some abuse women. They don't know the people on the streets like us. They just go after their target. We have suffered from this problem."

Accounts of older ISOF operations I heard around Baghdad suggest that the Americans may have knowingly allowed violence against civilians. In Adhamiya, long the stronghold of the Sunni insurgency in Baghdad, two hospital employees described their 2006 run-in with the ISOF to me. According to both witnesses, a self-identified ISOF operative named "Captain Hussam" unloaded his machine gun in the Al Numan Hospital after seeing the body of his superior, who had died under the hospital's care. An American operative with a red beard stood by silently watching. According to one witness, the Iraqi operative demanded his commander's death certificate, threatening to "torture you, kill you, and kill the people of Adhamiya" if they didn't comply. The witnesses said the eight operatives who entered the hospital were driving Humvees, vehicles that only the Americans and the ISOF use. The next day, Captain Hussam returned, a witness said, offering a box of bullets as an apology.

The effective head of the American ISOF project is General Trombitas of the Iraq National Counter-Terror Transition Team. A towering man with a gray mustache and a wrinkled brow, Trombitas spent nearly seven of his over thirty years in the military training special forces in Colombia, El Salvador, and other countries. On February 23, he gave me a tour of Area IV, a joint American-Iraqi base near the Baghdad International Airport, where US Special Forces train the ISOF. As we walk away from the helicopter, he cracks a boyish smile. Though he's worked with special forces all over the world, he tells me the men we are about to meet are "the best".

Trombitas says he is "very proud of what was done in El Salvador", but avoids the fact that special forces trained there by the United States in the early 1980s were responsible for the formation of death squads that killed more than 50,000 civilians thought to be sympathetic with leftist guerrillas. Guatemala was a similar case. Some Guatemalan special forces that had been trained in anti-terrorism tactics by the United States during the mid-1960s subsequently became death squads that took part in the killing of around 140,000 people. In the early 1990s, US Special Forces trained and worked closely with an elite Colombian police unit strongly suspected of carrying out some of the murders attributed to Los Pepes, a death squad that became the backbone of the country's current paramilitary organization. (Trombitas served in El Salvador from 1989-90, and in Colombia from 2003-2005, after these incidents took place.)

"The standards get looser when the Americans aren't with [the local special forces], and they can eventually become death squads, which I believe actually happened in Colombia," says Mark Bowden, author of Black Hawk Down and Killing Pablo, a book about the hunt for Colombian drug lord Pablo Escobar by CIA and US Special Forces. The tactics taught in each country are the same, Bowden says. "They teach the same kind of skills. They use the same equipment."

Trombitas told the official blog of the Defense Department that the training missions used in Latin America are "extremely transferable" to Iraq. Salvadoran Special Forces even helped train the ISOF, he tells me. "It's a world of coalitions," he says. "The longer we work together, the more alike we are. When we share our values and our experiences with other armies, we make them the same."

Trombitas guides me into a warehouse where ISOF operatives, most of them in black masks, have been preparing for our arrival. He walks me through a special display of their American equipment – machine guns, sniper rifles, state-of-the-art night-vision equipment, and fluffy desert camo – that makes soldiers look like teddy bears. He takes me up a catwalk overlooking a fake house stocked with cartoonish posters of big-breasted women pointing pistols, a couple of real men dressed as "terrorists" with kaffiyehs wrapped around their faces, and a 10-year-old boy playing hostage.

As we stand in the observation area, the door explodes. After a minute of constant shooting, the operatives march out with the "terrorists", the boy, and a poster of an '80s-style villain, wearing a jean jacket and holding a woman hostage. More than twenty bullet holes are centered on his forehead. "Look at that marksmanship," Trombitas says, smiling proudly.

Trombitas gets to the issue of human rights before I do. He assures me that US Special Forces take allegations of human rights abuses very seriously – two Iraqi men were let go for prisoner abuse since he took over in August last year, he says – but he won't comment on specific cases. I raise the issue of accountability and bring up one well-documented mission that caused waves in the Iraqi Parliament: in August, the ISOF raided Diyala's provincial government compound, reportedly with the support of US Apache helicopters. They arrested a member of the Iraqi Islamic Party, Iraq's main Sunni Arab party. They also arrested the president of the university, also a Sunni, and killed a secretary and wounded four armed guards during the night.

I barely get the word "Diyala" out of my mouth before the American operatives standing around us start to grumble nervously and a translator jumps in. "For the reputation of the ISOF, please, let's cut that off," he says.

Abdul-Karim al-Samarrai, a member of the ruling United Iraqi Alliance and the parliamentary Security and Defense Committee, says that what happened in Diyala was one of many signs of the prime minister's bad intentions for the ISOF. "Politicians are afraid because this force can be used for political ends," he says. In response to outrage from members of Parliament over the arrest of politicians by the ISOF, Maliki, who is officially required to approve every ISOF target, denied any knowledge of the Diyala mission. His claim of innocence raises important questions. If the man who is supposed to be in charge of the ISOF has no knowledge of its missions, then who is ultimately responsible for the force? Was Maliki lying to cover up the fact that he is using the force for political purposes? Or was someone else – namely the Americans – calling the shots?

Diyala was only the first publicized case of possibly politically motivated arrests. In December, the ISOF arrested as many as thirty-five officials in the Interior Ministry who were thought to be in opposition to Maliki's Islamic Dawa Party. This past March, the ISOF arrested at least one leader of the Awakening Councils, semiofficial Sunni neighborhood militias that have been increasingly at odds with Maliki over his failure to keep a promise to incorporate the councils into the military or give them other employment.

The Maliki government has developed a "culture of direct control," says Michael Knights, a Lafer Fellow at the Washington Institute and the head of its Iraq program. Knights visits Iraq regularly and has close contact with the country's security services. He says the people in charge of the ISOF at the regional levels are "personally chosen loyalists or relatives of Maliki. It reminds me of Saddam." Knights says that Maliki is only supposed to approve or reject missions that come to him, but occasionally he will "assert his prerogative as the commander in chief and tell the ISOF to do something or not to do something." Knights raises the possibility that the ISOF will become Maliki's personal death squad. "The prime minister is looking for re-election, and there are not that many restraints on his ability to target political opponents, as [his government] has been doing with the Sadrists for years now."

Samarrai, along with other members of Parliament, is calling for disbanding the Counter-Terrorism Bureau. He says there is no legal basis for an armed brigade to exist outside the control of the Interior or Defense ministry. "People are afraid of the existence of an organization with such dreadful capabilities that reports directly to the prime minister," he says.

Member of Parliament Hassan al-Rubaie is concerned about the close relationship between the ISOF and the Americans. "If the US leaves Iraq, this will be the last force they will leave behind," he insists. He is worried that such a powerful and secretive force that is closely tied to the Americans could turn Iraq into a "military base in the region" by allowing the United States to continue to conduct missions in Iraq with the cover of the ISOF. "They have become a replacement" for the Americans, he says.

President Obama has said he plans to increase reliance on the US Special Forces; Defense Secretary Robert Gates's recent appointment of Stanley McChrystal as commander of Afghanistan suggests that he is keeping his word. From 2003 to 2008, McChrystal was the head of the Joint Special Operations Command, which oversees the Army's most secretive forces and is responsible for the training of special forces abroad. McChrystal was also commander of US Special Operations Forces in Iraq for five years, during which time, according to the Wall Street Journal, he commanded "units that specialize in guerrilla warfare, including the training of indigenous armies."

"The eventual drawdown in Iraq is not the end of the mission for our elite forces," Gates said in May 2008. Gates hasn't spoken on the issue since Obama took office, but Obama says he will institutionalize irregular warfare capabilities, and the White House stresses the need to "create a more robust capacity to train, equip and advise foreign security forces, so that local allies are better prepared to confront mutual threats."

Bowden says those "local allies" are often used for covert operations. "The United States Special Operations Command cultivates relationships with special forces in other countries because it gives the United States the opportunity of intervening militarily in a covert way," he says. "The ideal covert op is one that is actually carried out by local forces."

As I stand on the tarmac with Trombitas in Area IV, waiting for our helicopter to return and fly us back to the Green Zone, I ask him how long the United States will be involved with the ISOF. "Special forces are special because we do maintain a relationship with foreign forces," he says. "Part of our theater-engagement strategy is to maintain a relationship with those units that are important to the security of the region and to the world." As our helicopter appears in the lightly clouded sky, he chooses his next words carefully: "We are going to have a working relationship for a while," he says.